A glimpse on the pattern of rodent diversification: a phylogenetic approach.

BACKGROUND: Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. RESULTS: Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. CONCLUSIONS: The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Code Generation for an Application-Specific VLIW Processor With Clustered, Addressable Register Files

International audienceModern compilers integrate recent advances in compiler construction, intermediate representations, algorithms and programming language front-ends. Yet code generation for appli\-cation-specific architectures benefits only marginally from this trend, as most of the effort is oriented towards popular general-purpose architectures. Historically, non-orthogonal architectures have relied on custom compiler technologies, some retargettable, but largely decoupled from the evolution of mainstream tool flows. Very Long Instruction Word (VLIW) architectures have introduced a variety of interesting problems such as clusterization, packetization or bundling, instruction scheduling for exposed pipelines, long delay slots, software pipelining, etc. These have been addressed in the literature, with a focus on the exploitation of Instruction Level Parallelism (ILP). While these are well known solutions already embedded into existing compilers, they rely on common hardware functionalities that are expected to be present in a fairly large subset of VLIW architectures. This paper presents our work on back-end compiler for Mephisto, a high performance low-power application-specific processor, based on LLVM. Mephisto is specialized enough to challenge established code generation solutions for VLIW and DSP processors, calling for an innovative compilation flow. Conversely, even though Mephisto might be seen a somewhat exotic processor, its hardware characteristics such as addressable register files benefit from existing analyses and transformations in LLVM. We describe our model of the Mephisto architecture, the difficulties we encountered, and the associated compilation methods, some of them new and specific to Mephisto

A glimpse on the pattern of rodent diversification:a phylogenetic approach

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. Results Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. Conclusions The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes

Brains, tools, innovation and biogeography in crows and ravens

BACKGROUND: Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative strategies and even use of tools in their search for food. The 40 Corvus species have also been successful dispersers and are distributed on most continents and in remote archipelagos. RESULTS: This study presents the first molecular phylogeny including all species and a number of subspecies within the genus Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success in applying tools when foraging and (ii) has some correlative role in the success of colonization of islands. Our results demonstrate that crows originated in the Palaearctic in the Miocene from where they dispersed to North America and the Caribbean, Africa and Australasia. We find that relative brain size alone does not explain tool use, innovative feeding strategies and dispersal success within crows. CONCLUSIONS: Our study supports monophyly of the genus Corvus and further demonstrates the direction and timing of colonization from the area of origin in the Palaearctic to other continents and archipelagos. The Caribbean was probably colonized from North America, although some North American ancestor may have gone extinct, and the Pacific was colonized multiple times from Asia and Australia. We did not find a correlation between relative brain size, tool use, innovative feeding strategies and dispersal success. Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances are right

TinyNode: A Comprehensive Platform for Wireless Sensor Network Applications

We introduce the TinyNode platform for wireless sensor networks. Supporting both research and industrial deployments, the platform offers communication ranges that exceed current platforms by a factor of 3 to 5, while consuming similar energy. It comes with a rich, practical set of hardware extensions and full TinyOS support. We describe the design choices of the TinyNode, the accompanying hardware modules, and the MAC layer implementation

Molecular phylogeny of South-East Asian arboreal murine rodents

peer reviewedRecent phylogenetic studies and taxonomic reviews have led to nearly complete resolution of the phylogenetic divisions within the old world rats and mice (Muridae, Murinae). The Micromys division and Pithecheir division are two notable exceptions where groupings of species into these divisions based on morphology and arboreal lifestyle have not been supported by phylogenetic evidence. Several enigmatic species from these divisions have been missing from molecular studies, preventing a rigorous revision of phylogenetic relationships. In this study, we sequenced for the first time one mitochondrial and three nuclear genes from South-East Asian keystone species of these two arboreal divisions: Hapalomys delacouri (Micromys division), Lenothrix canus and Pithecheir parvus (Pithecheir division). We also complemented the molecular data already available for the two divisions with new data from Sundaic Chiropodomys, Indian Vandeleuria oleracea and the recently described Sulawesian Margaretamys christinae. Using this new phylogenetic framework and molecular dating methodologies, our study allows some more detailed classification of the former Micromys and Pithecheir divisions, while confirming their polyphyletic status. Specifically, the former Micromys division should now be split into four monotypic divisions: Chiropodomys, Hapalomys, Micromys and Vandeleuria divisions. The former Pithecheir division is likely to be refined and restricted to Pithecheir and probably Pithecheirops, whereas Lenothrix and Margaretamys should now be recognized as representatives of the Dacnomys division. Our findings have profound implications with regard to the systematics of Murinae, as well as to the early evolution of murine morphology and dental characters

Mammalian maxilloturbinal evolution does not reflect thermal biology

The evolution of endothermy in vertebrates is a major research topic in recent decades that has been tackled by a myriad of research disciplines including paleontology, anatomy, physiology, evolutionary and developmental biology. The ability of most mammals to maintain a relatively constant and high body temperature is considered a key adaptation, enabling them to successfully colonize new habitats and harsh environments. It has been proposed that in mammals the anterior nasal cavity, which houses the maxilloturbinal, plays a pivotal role in body temperature maintenance, via a bony system supporting an epithelium involved in heat and moisture conservation. The presence and the relative size of the maxilloturbinal has been proposed to reflect the endothermic conditions and basal metabolic rate in extinct vertebrates. We show that there is no evidence to relate the origin of endothermy and the development of some turbinal bones by using a comprehensive dataset of µCT-derived maxilloturbinals spanning most mammalian orders. Indeed, we demonstrate that neither corrected basal metabolic rate nor body temperature significantly correlate with the relative surface area of the maxilloturbinal. Instead, we identify important variations in the relative surface area, morpho-anatomy, and complexity of the maxilloturbinal across the mammalian phylogeny and species ecology

Phylogeny and historical biogeography of gnateaters (Passeriformes,\ud Conopophagidae) in the South America forests

We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of the genus Conopophaga. The phylogenetic analyses support the reciprocal monophyly of the two genera, Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae suggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga clade was highest in the late Miocene, followed by a slower diversification rate, suggesting a diversity-dependent pattern. Our analyses of the diversification of family Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatio-temporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.We thank John Bates (FMNH) and Nate Rice (ANSP) for providing some of the tissues used in this study. We thank Fernando M. d’Horta, Renato G. Lima, Gustavo S. Cabanne, and Guilherme R. Brito for collecting some samples used in this study. Amy Chernasky from Lynx Edicions kindly provided permission to use images from Handbook of Birds of the World. We thank Gustavo Bravo for suggestions on previous version of the manuscript. We thank an anonymous reviewer and the Editor Carey Krajewski for their comments. This study was co-funded by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) (2009/12989-1, BIOTA 2013/50297-0), NSF (DOB 1343578), NASA, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). JF and PHF thanks the Danish National Research Foundation for funding the Center for Macroecology, Evolution and Climate; PGPE and MI thanks the Swedish Research Council for funds (Grant No. 621-2010-5321 to P.G.P.E.). PHF was supported by Marie-Curie grants (PIOF-GA-2012-330582-CANARIP-RAT, FP7 CIG-293845). Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (IBAMA) and Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio) provided permits to collect the samples. This work was developed in the Research Center on Biodiversity and Computing (BioComp) of the Universidade de São Paulo (USP), supported by the USP Provost’s Office for Research

Inférence des processus de diversification au sein des Mammifères (l'intérêt des méthodes phylogénétiques macroévolutives appliquées aux Rongeurs et Primates)

Une question fondamentale en biologie de l'évolution est de comprendre pourquoi certaines lignées sont très diversifiées et d'autres non. Pendant de nombreuses années, les études du registre fossile ont permis de quantifier les patrons de la diversité du vivant ainsi que les tendances majeures de la spéciation et de l'extinction au cours du temps. Avec l'expansion de nos connaissances concernant l'arbre du vivant, le développement de nouvelles méthodes qui ne se réfèrent pas au registre fossile ont permis d'appréhender ces processus de spéciation et d'extinction. Ces méthodes ont permis de jeter un regard nouveau sur l'histoire macroévolutive des Mammifères. Au sein des Mammifères, les Euarchontoglires représentent le clade le plus diversifié à l'heure actuelle. Au cours du Tertiaire, les Euarchontoglires ont connu une extraordinaire radiation adaptive qui leur a permis d'occuper des niches écologiques très différentes et de se répandre, dans le cas des Rongeurs, sur l'ensemble des continents. Peu d'études se sont intéressées à la macroévolution des Rongeurs et à l'inclusion des données du registre fossile des Primates pourtant très étudiés. Les Euarchontoglires représentent donc un modèle de choix quant à l'inférence des processus de diversification et l'estimation des variations du taux de spéciation au cours du temps. Ici nous présentons pour la première fois une études macroévolutive des Rongeurs et des Primates réalisé à l'aide d'une approche mixte de supermatrice et de superarabre. L'utilisation de l'ensemble des bases de données nucléotidiques pour ces deux ordres a permis l'obtention de phylogénies résolues pour 80 % des espèces de Primates et 60 % des espèces de Rongeurs. Les arbres que nous avons ainsi obtenus nous ont permis d'appliquer des méthodes d'horloge moléculaire relâchée afin de dater les évènements de spéciation au sein de ces clades, puis d'appliquer des méthodes de macroévolution. Nous montrons ainsi l'hétérogénéité du taux de spéciation au sein des Rongeurs vis-à-vis des Primates. Des accélérations du taux de diversification au cours du temps ont été découvertes et analysées chez les Rongeurs et chez les Primates. Elles ont révélé un nombre important d'épisodes de diversifications chez les Muridae + Cricetidae pour les Rongeurs, et les Cercopithecidae chez les Primates. Le lien qu'il existe entre le taux de spéciation et des facteurs de diversification ont été testés. Ainsi l'impact des colonisations et de la masse corporelle sur le taux de diversification a pu être évalué. Ces deux facteurs ont influencé à leur manière le taux de spéciation, mais n'expliquent évidemment pas toutes les variations observées. L'un des résultats important de ces analyses de diversification concerne l'influence de l'extinction sur les estimations des paramètres macroévolutifs dérivés des phylogénies d'espèces actuelles. La réalisation d'un superarbre des Primates fossiles et actuels a d'ailleurs permis de mettre en évidence quelques sources potentielles d'erreur dans les analyses macroévolutivesA fundamental question in evolutionary biology is to understand why some lineages are highly diverse and others are not. For a long time, the study of fossil record provided an insight into the pattern of diversification and revealed major trends of speciation and extinction through time citep{Alroy:2008,Sepkoski:1981}. With the expansion of our knowledge about the tree of life, the development of phylogenetic methods that do not rely on fossils allowed for the studying of the evolutionary process through time. In fact, the use of a dated phylogenetic tree with exhaustive taxonomic sampling allows for the estimation of both extinction and speciation rates and to detect accelerations in diversification rates. These kind of methods have shed light to macroevolutionnary patterns for a lot of clade Mammalia. Within the Mammalia, the Euarchontoglira is the most diversified extant clade. Throughout the Tertiary, Euarchontoglira underwent an extraordinary adaptive radiation that led them to represent one half of mammalian diversity and to spread over all continents and terrestrial ecosystems. Despite the increase attention for diversification studies, no clear phylogenetical frameworks have adressed the case of the most diversified mammalian clade : the Rodentia and no clear paleontological integration have studied the extinction parameter within the well studied Primate clade. More precisely, Euarchontoglira represent a suitable model to identify the factors that could have enhanced morphological diversity and speciation rate. Here, we present a new Rodent and Primate phylogeny inferred from a molecular supermatrix analysis including 60 % of Rodent species diversity and 80 % of the Primate diversity. The resulting phylogenetic trees were subsequently dated with a relaxed molecular clock approach in order to provide a time framework for speciation events. Results obtained from relaxed molecular clock analyses concurred with previous dating works using the same fossil constraints. The resulting timetree allowed us to apply macroevolutionary methods and to compare macroevolutionary processes among the rodents and primates. We investigated the diversification rate constancy hypothesis, the diversification rate heterogeneity and the shifts in diversification rate. Rodents have a greater degree of variation in their among clade diversification rate than any other mammalian clades previously studied and depart from the constant diversification hypothesis. This pattern is not recover from the Primate phylogeny. We located shifts in diversification rate within the major clades of primate and rodents especially within Muridae and Cricetidae for the rodents and especially so within Cercopithecidae for Primates. We then explored weither some branches leading to clades with significant increase in diversification rate might be associated with dispersal into geographic regions. We found nine significant accelerations for Rodents and three for Primates co-occurrent from colonization events and we showed that colonization have minor impact on diversification rate. Our results demonstrated that rodents and primates undergone shifts in diversification rate regularly through the Tertiary, but at different periods considering each clades. A comparison between the rodent fossil record and our results suggest that extinction lead to the loss of diversification and colonization signals for most of the Paleogene nodes. The inclusion of fossil within an extant primate phylogeny display the major impact of ectinction on estimation of speciation parameters from extants species phylogeniesMONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF